Kyogre can be found in the Marine Cave. A man at the Weather Institute will explain that one of four routes is experiencing "abnormal conditions". If you do not get to the cave in time, the Terra Cave will appear instead. Once Groudon is battled and/or caught, Marine Cave will "reappear and relocate".
Latios can either be found roaming or on the Southern Island. You can receive the Eon Ticket to get to Southern Island from Norman after defeating the Hoenn League. This was only part of an event, however, so you cannot obtain the second Lati if you did not take part in this event.
Hope I helped!